Scholarly Communications

Learn about trends in scholarly publishing and communication.

Compliance requires

  • Manuscripts resulting from NIH funding are submitted to the NIH Manuscript Submission system (NIHMS) upon acceptance for publication and that all NIHMS tasks are complete within three months of publication.
  • Full-text of final peer-reviewed manuscripts or final published articles resulting from NIH funding is available in PubMed Central within one year of publication.
  • PubMed Central Identification numbers (PMCID) are used in biosketches, reports and grant applications to show compliance.
  • UPDATE! See the slides or transcript from a 1/15/13 webinar titled Changes to the NIH Public Access Policy and the Implications.

Pre-publication Step 1: Get Organized

  • Make a list of all of the people involved in the grant, their institution affiliation and email address and their administrative contacts if necessary. As the Principal Investigator (PI) you are responsible for any manuscripts arising from this research grant, including trainees’ publications, even if you are not an author.
  • Communicate the submission process to all members of the team and determine who will submit the manuscripts in PMC.
  • If not already established, create a My NCBI account to gain access to My Bibliography to manage your citations and the submission process.

Pre-publication Step 2: Understand and use the appropriate copyright transfer agreement

  • Before you sign a publication agreement or similar copyright transfer agreement, make sure that the agreement allows the manuscript to be posted to PubMed Central in accordance with the NIH Public Access Policy.
  • Please use the Hopkins Authors' Addenda.
  • Recommended: The broader addendum retains more rights for authors.

Manuscript Accepted Step 3: Determine which submission method you need to follow

Start this process immediately upon acceptance for publication. Submission *MUST* be completed within three months of your manuscript being published.

Submission Method A: The journal deposits final published articles in PubMed Central without author involvement.

  • Check the PubMed Central list of journals to see if the journal submits on your behalf. If the journal is on the list you do not need to initiate submission. Once the process is completed, the PI will receive a PMCID number by email.
  • If a journal is not on the PMC journal list, check the journal's web site for their NIH policy statement. If the journal says they will deposit on your behalf even though they are not on the PMC list, you do not need to initiate the submission process. However, you may need to approve the submission process (see Submission Method D).


Submission Method B: You ask the publisher to submit the manuscript for you, generally for a fee.

  • If the journal is not on the automatic submission list and you want the journal to deposit on your behalf and you are willing to *PAY* for this, check to see if your journal is published by one of these publishers.
  • Contact the publisher to arrange the submission.


Submission Method C: If none of the above applies, you will need to submit the manuscript.
With this method there are three tasks to be completed. Task one can be completed by someone other than the author. Tasks two and three must be completed by the author.

Task One: Deposit manuscript files and link to NIH funding.

  • Determine which version of the paper you need to submit. Most journals require that you deposit the final peer-reviewed manuscript. This is the paper that was accepted for publication, not the final published article.
  • Upload a copy of the accepted final peer-reviewed manuscript and associated files into NIHMS using My NCBI, My Bibliography.
  • Information you will need for submissions:
    • Principal investigator name and email address
    • Title of the journal
    • Title of the manuscript
    • Grant number(s)
    • Confirmation (copy of signed publisher/author agreement) that you have copyright clearance to comply with the NIH Public Access Policy
    • Manuscript file(s) (Word, Excel, PowerPoint, TIFF, GIF, JPEG, PDF, etc.)
    • Embargo period (how long after publication can the article be made available in PMC per publisher. This information can be found on the journal's website.

Task Two: Authorize the NIH manuscript

  •     The author will receive an email requesting authorization for NIH to process the manuscript.


Task Three: Approve the PMC-formatted manuscript for public display.

  •     The author will receive an email requesting approval of the PMC-formatted manuscript. Any changes or corrections can be made at this time.


Following Completion of Task Three:

  •     The NIHMS will email the author and all the PIs the citation with the PMCID once it is assigned.
  •     PMC will automatically make the paper publicly available after the designated delay period has expired.


Submission Method D: The publisher deposits the manuscript files, but provides contact information for the corresponding author to authorize and approve the submission process.

  • Though a publisher may make the initial deposit of files under Method D, NIH awardees are responsible for ensuring that manuscripts are submitted to the NIHMS upon acceptance for publication and that all NIHMS tasks are complete within three months of publication.
  • The NIHMS will notify the author when the manuscript files are received from the publisher. At that point, the author must complete all of the tasks outlined for Method C, except for the file deposit part of Task One above.

Step 4: Tracking the Manuscript

  • If you received a temporary NIHMS number, this number will be replaced with a PMCID number once the submission process is completed. The NIHMS number is only valid for up to three months after the manuscript is published.
  • The PMCID is posted in PubMed as soon as an article has been successfully processed by PMC, which usually occurs around the time of publication. PMCIDs are listed in the lower right corner of the AbstractPlus view in PubMed.
  • You can quickly locate PMCID numbers using the "PMC to PMCID" converter tool.
  • If you use RefWorks to manage your citations, exporting from PubMed or PubMed Central will include the PMCID. The NIH output style will include the PMCID in your ctations.
  • If you use ENdNOte to manage your citations, EndNote X3 and later come wtih updated files that import the PMCID to the PMC filed automatically. For older versions of EndNote, you will need to download an import filter and output style from EndNote's website.

Step 5: Citing the Manuscript

You are required to provide the PMCID number when citing your papers in biosketches, NIH applications, proposal, and reports. The appropriate citation is to list the PMCID number at the end of the full journal citation for the paper.

For example:
Staiger DO, Auerbach DI, Buerhaus PI. Comparison of physician workforce estimates and supply projections. JAMA. 2009 Oct 21;302(15):1674-80. PMC2791886.

For papers published more than three months the PMCID is the only way to demonstrate compliance.

If you have not yet received a PMCID number because the paper is in press, or is published within three months of when an application, proposal or report is submitted, use the following in your citation:

  • If the journal has submitted the paper for you and you have not received the PMCID number, use: “PMC Journal - In Process”.
  • If the journal is not on the approved “automatic submission” list but has been submitted on your behalf, you will need to provide a valid NIHMSID number (not more than three months old).
  • If you submitted the manuscript, you will need to provide a valid NIHMSID number (not more than three months old).